The Thirteenth Doctor Chronicles - Part One - Thirteen Begins
by the stargate time traveller
Summary: A new series I'm working on of short stories of the Thirteenth Doctor. The regeneration of the Twelfth Doctor and shortly before she recovers her TARDIS.
1. Chapter 1

Disclaimer - I don't own Doctor Who, I just own this story. The drill should be familiar to you by now.

Feedback, always appreciated.

A/N - As far as the Doctor is concerned, Missy went with the Master. He doesn't know she was planning on standing with him against the Cybermen during that battle. Ophiuchus was a Time Lord healer who is responsible for Time Lords like the Master and the Doctor having more regenerations, Drax is another renegade who was in the same class as the Doctor and the Master. The Eleven was a Time Lord who's played by Mark Bonnar on the Big Finish productions; he is a Time Lord who suffers from a condition where he can hear all the personalities he has had over the centuries, which have driven him and his other selves insane.

* * *

The Thirteenth Doctor Chronicles.

Thirteen Begins.

_The problem with regeneration is you have no idea what you're going to get out of it, _the Doctor, currently in the final moments of his twelfth incarnation, thought to himself as he took one last look around the TARDIS console room, unable to believe it was happening. He was about to regenerate, although he had known he would change once more, losing another lifetime in the process.

The Doctor had known about his impending regeneration for a while already.

Back on the Mondasian colony ship - he still wasn't sure if the TARDIS had taken him back in time in relation to Mondas' timeline, or if the Mondasians had contacted an alien race for help since the ship itself was _massive, _and because he knew that Earth's twin planet could not have constructed such a ship of such size and complexity and still have enough resources to create the first Cybermen and be strong enough to endure the original journey to Earth - when he had been critically injured by the Cybermen after the Master and Missy had both left him to die.

Only he didn't want to regenerate.

The Doctor had become _tired_ of running around for a few hundred years in _one body, _with _a single __**unique **_personality, only to become critically injured and having to regenerate again.

Indeed, when he had learnt he was regenerating for real again, he had tried hard to avoid the change. It wasn't difficult and yet it wasn't easy, he was able to delay the change by either forcibly willing the energy away, or shoving his hands into snow.

He had had enough!

He didn't want to regenerate.

He didn't want to be somebody else. It had taken him ages before he had recovered enough to accept the conflict in his new life and accept who he was in this new life; in his last few lives, the Doctor had been travelling the universe alone, so sure he was the last of his race after the Time War. When he had discovered he had saved his people, he had been delighted until that mess with Rassilon and Clara during the last time he had been on Gallifrey.

But the thing was, he had every reason to be conflicted given this regeneration had been the start of his second regeneration cycle.

It was very rare for Time Lords to accept additional cycles; the Master had only received one because the Time Lords had wanted to use him and his skills, although it seemed the idiot had learnt to be more…._restrained _with his new lives, he had not been running around like he had been before, burning through his lives without a care in the universe.

Frankly at this point, the Doctor truly didn't care how the Master, or Missy, depending on which incarnation he thought of though he would do his best _not _to think about the disaster he had just been through, how he had made the mistake of trusting Missy after having her in the Vault at the university, and thinking he could rehabilitate her.

He should have known better, but then again how was he meant to know her previous incarnation was on the ship?

He winced as he suddenly felt another burning surge of regeneration energy pouring through his cells like a volcanic reaction. He might have described regeneration to Peri as a violent biological reaction, but in truth, it was a lot more powerful than that. At the moment the Doctor likened the burning heat he was going through as a contained solar flare inside his chest.

Regeneration was one of the most painful experiences a Time Lord had to endure, but as the old expression said _no pain, no gain. _And it was a tremendous, agonising experience. You feel a burning sensation, and you feel as if all of your organs are being burnt but turned inside out, squashed or expanded into a new shape while you feel as if your bones were about to implode and explode at the same time.

The agony was more than enough, but the worst came afterwards. Some times a Time Lord who had more control could weather out the storm of the regeneration and recover quickly, but the Doctor had always hated regeneration even before now. Right back to his first incarnation. The Doctor sniffed a little bit as he thought about his first incarnation, the same incarnation whom he had just met, a man so ignorant about the scale of the journey he was about to take - the exile to Earth, the mess when the Time Lords had wanted him to defeat Omega, the agonising death of his third incarnation, the Key to Time fiasco, the Last Great Time War among other things, and everything that had followed since. An incarnation who enjoyed acting and sounding like a pompous university professor with an arrogance the Twelfth Doctor knew had been shared by some of the other incarnations scattered up and down the line.

But all of his incarnations shared the first's attitude toward regeneration.

When the Doctor had been at the Time Lord Academy as a student with no clue about what his future would hold, he had always been frightened by regeneration, learning that the process would alter the personality a bit and shift it around as the process seemed to cherry-pick the best things that matched without any consideration that the previous Time Lord had been settled.

It was a process the Doctor had always tried very _very _hard to avoid.

The idea of losing an incarnation was bad enough, but the thought of an established personality going through the regeneration and then being relegated to the back of the Time Lord's mind….

The Doctor cast his eyes over the console while he was trying very hard not to collapse; he could feel the regeneration energy coursing through him, and he wished he had the time to divert the TARDIS. Land somewhere wide and open where the only damage would be the landscape. He remembered how, a couple of regenerations ago, the blast of energy had devastated the TARDIS console room, and it had taken a long time before the TARDIS had recovered enough to travel properly.

But there was no time.

The Doctor took a deep breath as he started to finish the speech he was making for his next incarnation. He knew he should have just gotten on with it, but he had not wanted to just regenerate as soon as he had stepped into the TARDIS and put the old girl into motion, he had wanted to set the controls to send the TARDIS to a deserted location where he could regenerate in peace. He had figured that since he had been regenerating for some time, he would have the time. He had the feeling the TARDIS, sensing trouble since the last time he had regenerated had seen him lose a large amount of energy until all he had needed to do was change his appearance, had gone to the South Pole, though he should have known she would have had good reasons to arrive at the eve of his first-ever regeneration. The TARDIS had a long memory, she would probably have remembered the agony she had been in the last time he had crippled her with a regeneration, and she wouldn't have wanted to go through it again. Unfortunately, it wasn't meant to be.

He sighed.

It was time.

"Doctor," he said quietly as he looked around the console room, wishing either Bill or Clara were here although it was a bad idea since what was about to happen was not going to be good, "I let you go."

Holding his hands outstretched in the traditional regeneration posture to reflect the energy away from himself, the Doctor let the barriers drop. Instantly his vision became clouded with the burning glare of regeneration, his eyes burning both from the brightness of the light and the searing heat of the energy itself as it burned through his eyes, and he could feel his skin, muscles and bone on fire while he felt a sudden change of gravity.

_Oh no, _the Doctor thought, realising what was happening even while being aware of the explosions going on, although with the rush of energy it was hard to be sure of what was being destroyed.

_Oh, not the TARDIS. Not again… Hold on, is that hair that's now in front of my face…blonde?! Ooh, I haven't been blonde in years! _

New thoughts, new ideas were coming into the Doctor's head, memories of past adventures pouring into the mind as the regeneration went on.

The Doctor remembered a few adventures during his first and second lives as they had both travelled through the universe before the exile to Earth when they had been grounded for a spell; he remembered a trip in the TARDIS with Romana (oh, those were the days), and that mess with Ophiuchus among other things, when the Time Lord healer had been trying to extend the typical twelve-regeneration limit of the regeneration cycle.

Other adventures entered the Doctor's mind as the regeneration started to finish and then it was over. The Doctor staggered, feeling like a puppet whose string had just been sliced through with a pair of scissors, but the Time Lord couldn't help it. The Doctor estimated that a good half of the last height had just been taken away, and now the second incarnation of his new regeneration cycle was shorter.

Distantly the Doctor heard a metallic ching, but he was too distracted to pay much attention as he staggered around, trying to get used to the centre of gravity in his new body.

He'd had it all. He had been young, he had been middle-aged, he had been ancient, all physically and he had grown accustomed to it all. Just like he had grown used to being tall, thin, short, even a bit overweight. But it had been years since he had been short. The last incarnation to be quite short had been his seventh incarnation, before the Time War; all subsequent lives had been taller.

The Doctor took a few deep breaths, wincing a little bit at the left-over tremors of pain from the main regeneration. As he exhaled, he noticed a strange _weight on his chest, _and there was also a strange…sensation between his legs.

_What? _

Moving on unfamiliar legs to the console - the Doctor hoped to spend some time walking to get used to walking with these unfamiliar legs with the new height - the Doctor only just managed to grab one of the scanners and pull it around. The screen wasn't the perfect mirror, but it was enough for the Doctor to see his new….appearance.

What he saw in the mirror made him think for a second he was seeing things, some form of old, classic post-regeneration hallucination, but the Doctor knew it wasn't; rapid blinking and pushing the will forward through the symptoms already being experienced saw to that; ever since the early days of his eleventh incarnation he had been significantly better post-regeneration, and this was no exception.

What the Doctor was seeing in the screen….was real.

The Doctor gaped and pulled away from the screen after taking a good look at the screen. He….was not a he, not anymore. He was now a _she. _Thirteen incarnations as a man, now she was a _she. _

Although gender as a concept was fluid in Time Lord culture, it was incredibly rare for any Time Lord to regenerate into a Time Lady, which made it very very rare for those like the Corsair (the Doctor had to fight back the surge of sadness at the thought of how her old friend had met his final death; the Corsair may have been a rogue, but the Doctor wouldn't wish what had happened to him on anyone, except perhaps Davros) to adjust to a gender other than the one they had been born into.

But the Doctor had known of other Time Lords who had regenerated into female bodies.

The Master was only one of them, though the Doctor had no idea if that had been a conscious choice or not. She didn't really care either at this point. What about Borusa, a Time Lord who might have made a mess of Time Lord politics during his presidency? Drax had been a male for the majority of his lives, but one of his regenerations had been a woman, although the Doctor still _wasn't _entirely sure which incarnation it was, and since that version of Drax had only appeared once, the Doctor still wasn't sure about the order of regenerations.

Thinking of old friends reminded the Doctor of Ophiuchus and the Corsair.

The Doctor didn't know why Ophiuchus had chosen to regenerate into the body of a woman when he had learnt he was dying, at least until the Doctor's fifth self had channelled energy into that chamber which gave Ophiuchus a new regeneration cycle, which was the culmination of Rassilon knew how many years of work to provide for the Time Lords, not that the High Council had liked it since it threatened their power base. But Ophiuchus' legacy lived on in Time Lords like the Doctor, and most recently the Master, though she wasn't sure just how many Time Lords the Council had offered new cycles to.

It probably wasn't that many, the Doctor reflected since many Time Lords were content with the one regeneration cycle.

_Though for others, regeneration is more of a curse than a blessing though its relative for all of us, _the Doctor reflected as she turned her now-healing brain over to the Eleven who then regenerated into the Twelve. It had been a long time since the Doctor had thought of that renegade; with most Time Lord incarnations, you knew they were the same person but they were different. The Eleven's lives…. they were all different people, psychos, thieves, and weirdos.

But now…

The Doctor had often considered regenerating into a female body despite being more confident in a male body, but ever since her second regeneration cycle had been given to her, the Doctor had thought about having a female body. She just didn't expect it to be this quick.

A slow but wide smile spread across her now young and smooth skin - ooh, it was good to be young again.

"Aw, brilliant!" the Doctor smiled and she tapped the console. Suddenly the console exploded and the TARDIS shifted, throwing her to the ground.

The Doctor gasped as she found herself with her cheeks pressed against the floor grating before the TARDIS console room pitched again and she started sliding backwards.

The Doctor gasped as she tried fruitlessly to grab hold of the grating, but her hands were still unfamiliar and she couldn't slip her fingers into the holes while she saw multiple electrical fires starting everywhere, and she frantically tried to get hold even as she slid down the floor as the TARDIS pitched. Somehow, miraculously, she managed to avoid the open doors, and grab the console; if she could stabilise her ship….

But it was hard as she had trouble standing on her feet, and pages torn from the collection of books she had around the room blew into her face through the open doors.

Gasping, she turned her head to look out of the doors when she heard a terrible sound like shattering glass and small explosions and she turned, only for her eyes to shoot open with horror at the sight of the _time rotor itself on fire and exploding. _No! The Power of the TARDIS….NO! How could her former self have been so STUPID!? Instead of just regenerating instead of hating the thought of losing his personality, he had delayed the inevitable, and now this was the result.

The Doctor screamed as the console panel came loose and she fell through the open doors of the TARDIS, just as a series of explosions ripped their way through her ship. She looked up and watched in horror as she took in the fires inside the console room before the TARDIS dematerialised, leaving her to fall through the air. She knew she was travelling through Earth's part of the vortex, but she didn't know where and when she was.

What a wonderful start to her new life.


	2. Chapter 2

Thirteen Begins.

As she stood outside Graham and Grace's house drinking tea with Graham, Ryan, and Yaz, the Doctor felt she really did not belong here; it had been bad enough at the funeral since she knew it was her fault Grace was gone. Alright, so she hadn't told Grace to endanger herself like that and getting electrocuted, but at the same time the Doctor knew she could have simply found a way of dealing with the Stenza on her own, but with her depleted resources and no idea of who she was thanks to a bout of post-regeneration amnesia which had been comparatively mild when you compared it to that mess when she had regenerated into her eighth incarnation (the Doctor had to hide a smile there, reminded of another Grace, only that one had been more cynical about the original dream she'd had to hold back death), only this time she hadn't had the shock of the Eye of Harmony being opened to restore her memory, she had felt she had needed the company.

In any case, the Doctor had felt she owed it to Grace even if she hadn't known the woman that well, the woman had been so kind-hearted, generous; she had even put the Doctor on the sofa when her post-regeneration sickness had gotten too much to handle, so she had attended the funeral even if she was certain Graham, Yaz, and Ryan held her responsible for what had happened to her.

She wouldn't blame them either.

_Another death on my conscience. _

The Doctor looked curiously at Graham as she remembered something he had said; she was curious, and since she wasn't going to be here long she decided to find out a few more things before she used the Stenza technology to try to track down the TARDIS from where she had lost it.

"What did you mean in your speech that you thought you'd run out of time?" she asked.

Graham looked startled by the question and explained in a reminiscent manner. "Well, I had cancer. Well, strictly speaking, I'm still in remission. Three years gone," he added, looking both sad and frightened at the reminder of his own mortality, though the Doctor could hardly blame him; she knew how it felt to be reminded of her own mortality, and she had felt it each and every time she had met one of her other incarnations and regenerated later down the line.

"Grace was my chemo nurse," Graham went on, looking both sad and happy as he remembered meeting his wife, "that's where we met and fell in love. So by rights, I shouldn't even be here."

The Doctor looked sympathetically at Graham before she looked away into the distance lost in thought as she considered what she had just learnt. She had never understood why humans relegated a particular idea of romance into a fairy tale mould, but the Doctor had a different idea of what made a fairy tale. As she thought about it, the Doctor couldn't help but be reminded of Richard Lazarus whom she'd met a couple of regenerations ago, but there were many differences between Graham and Lazarus; one of them had fought hard because he had found someone to believe in, the other had been arrogant and had wanted to be immortal because he genuinely couldn't face up to the fact everything had to die.

"Have you got family?" Yaz suddenly asked and the Doctor glanced at her, genuinely taken aback by the sudden question.

"No, lost them a long time ago," the Doctor replied after a moment's thought, though she wasn't sure if that were true; she hadn't really spoken to any of her family even after her exile to Earth had lifted and she had been allowed to go wherever she'd wanted without worrying about her people snatching her out of her time stream and punishing her again. Her third incarnation had tried to reach out following Omega's defeat, but she hadn't received any reply.

And over the centuries she had received nothing from them. During the Time War, her wartime incarnation had been more focused on dealing with the Daleks, though there had been moments when her wartime incarnation had investigated to see if her family were alive, though she couldn't find anything for definite.

Now she had no idea if she were the last of her family or not, though the thought was as depressing as thinking she was the last Time Lord, though now she wasn't sure what was worse.

"How do you cope with that?"

_I don't. _

The Doctor swallowed her immediate reply. "I carry them with me," she replied, deciding it was best not to mention she preferred thinking about them long before she had left Gallifrey; at least then she hadn't left and embarrassed the family. "What they would have thought, and said and done, make them a part of who I am. So even though they're gone from the world, they're never gone from me."

"That's the sort of thing Grace would have said," Graham smiled with a tinge of sadness at the wisdom of his wife.

The Doctor smiled back sympathetically while silence fell over the group, while the Doctor was left thinking about her family. Were they alive? Were they still on Gallifrey, trapped at the end of the universe? What were they doing now?

"So everything we saw, everything we lied to people about," Yaz once more interrupted the Doctor's thoughts, looking more uneasy because as a police officer everything they'd done was against the grain before she focused pointedly on the Doctor, "Is this normal for you?"

The Doctor couldn't help the smile appearing on her face - she was starting to really like being youthful in this body again after having a much older incarnation between her and her eleventh incarnation - as she looked at Yaz, though she felt sad knowing she was going to leave them soon. She had a few ideas after she had seen the Stenza technology on how she could use it to get the TARDIS back, but the sooner she left the better and they could go their own separate ways.

It was better that way.

"I'm just a traveller," she said simply. "Sometimes I see something that needs fixing, I do what I can."

The Doctor paused for a moment as she thought about that little description of herself she'd given to them. When it came down to it, she preferred thinking about those long-ago days where she had just travelled around, dealing with immediate situations, and then leaving as soon as she could. Even after the Time War, she had preferred that type of life even without any other Time Lords to monitor the universe and the timelines, but there had been moments where events were complex than she would have liked; that long, multi-century war in her eleventh incarnation against the Silence had been an example of how bad things had gotten, though there had been close contenders.

"Except right now, I'm a traveller without a ship," she went on, feeling the dull ache she felt in her chest at the absence of her TARDIS. "I've stayed too long," she said, starting to pull away, "I should get back to finding my TARDIS."

She was about to leave and make her way back to the garage where she'd had the resources to forge a new sonic screwdriver - it might be more primitive than the screwdrivers she'd had in the past, but it was good to have something familiar back in her grasp again now she'd practically lost everything -to see what she could make out of that Stenza technology there when Yaz said, "Doctor, can I just say..," she trailed off awkwardly as if wondering how best to say whatever was on her mind.

The Doctor stopped and turned and wondered what Yaz was about to say.

"…you really need to get out of those clothes."

Surprised the Doctor looked down at her clothes, she had been wearing the tattered remains of her twelfth incarnations clothes ever since she'd regenerated, but with the temporary loss of memory and the subsequent fight with Tim Shaw, the Doctor hadn't really given much thought about her clothes, although she had pushed away her irritation that the coat was too heavy on her and weighed her down, and she had occasionally trod on the hem of her trousers. She had hoped to leave Earth and recover the TARDIS where she could change her wardrobe.

At the same time, she had hoped to spend that time trying to find out how her new gender would affect her long term.

She ignored the snickering from either Graham or Ryan or both.

"Right, yeah," the Doctor said awkwardly as she looked up. "Been a long time since I brought women's clothes."

The Doctor had no idea what her new life would bring her, but she hoped it was long and happy one; most of her previous lives had lived for a long time, but it was starting to look up.


End file.
